So you want to run your site from a sub-directory on your FTP, but you do not want to have that directory display as part of your web address? Well, the solution is very simple (and does not even need a manual .htaccess change) and I am surprised I did not discover this sooner.
In your configuration.php of your Joomla! site, edit the $livesite parameter value, and do not leave it empty. You will then add your address without the sub-directory in the address, eg. if you website sits in
domain.com/joomla/ and you want to display only
This will display all URL's on the site without the sub-directory. Simple.